Variant report

Variant	rs2007683
Chromosome Location	chr6:36101562-36101563
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36100220..36102559-chr6:36104704..36106593,2	MCF-7	breast:
2	chr6:36099611..36101703-chr6:36163154..36166410,4	K562	blood:
3	chr6:36089580..36092157-chr6:36100589..36102722,2	MCF-7	breast:
4	chr6:36100003..36101717-chr6:36213418..36216121,2	MCF-7	breast:
5	chr6:36097672..36103046-chr6:36163327..36166048,5	MCF-7	breast:
6	chr6:36099568..36102831-chr6:36104693..36107135,4	MCF-7	breast:
7	chr6:36098131..36102554-chr6:36163258..36166179,4	K562	blood:
8	chr6:36097197..36101295-chr6:36101453..36104026,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000096070	Chromatin interaction
ENSG00000246982	Chromatin interaction
ENSG00000156711	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10447375	0.85[AMR][1000 genomes]
rs10447396	0.93[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1059227	0.93[ASW][hapmap];0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947589	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12193895	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12199702	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12201042	0.81[AMR][1000 genomes]
rs12201072	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12210904	0.87[AMR][1000 genomes]
rs12210946	0.83[ASN][1000 genomes]
rs12525283	1.00[JPT][hapmap]
rs17715809	1.00[JPT][hapmap]
rs2859135	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2859136	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2859137	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2859141	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711433	0.86[AMR][1000 genomes]
rs6940723	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3363467	chr6:35820920-36222197	Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2007683	KIF6	cis	cerebellum	SCAN
rs2007683	MAPK13	cis	Skin Sun Exposed Lower leg	GTEx
rs2007683	RP1-179N16.6	cis	Whole Blood	GTEx
rs2007683	CLPS	cis	parietal	SCAN
rs2007683	MAPK13	Cis_1M	lymphoblastoid	RTeQTL
rs2007683	MAPK13	cis	Esophagus Mucosa	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36098200-36107000	Weak transcription	HSMMtube	muscle
2	chr6:36099200-36117400	Weak transcription	Psoas Muscle	Psoas
3	chr6:36099600-36102000	Enhancers	Fetal Kidney	kidney
4	chr6:36099800-36101600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
5	chr6:36099800-36101600	Enhancers	NHEK	skin
6	chr6:36099800-36104200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:36099800-36104400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:36099800-36107400	Weak transcription	Fetal Brain Male	brain
9	chr6:36099800-36107400	Weak transcription	Fetal Brain Female	brain
10	chr6:36099800-36107600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:36099800-36113400	Weak transcription	Right Atrium	heart
12	chr6:36100000-36101600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr6:36100000-36102600	Weak transcription	HMEC	breast
14	chr6:36100000-36103000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:36100000-36104400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr6:36100000-36109600	Weak transcription	Brain Anterior Caudate	brain
17	chr6:36100200-36102000	Genic enhancers	Gastric	stomach
18	chr6:36100200-36102800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr6:36100200-36102800	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr6:36100200-36105800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:36100200-36108200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr6:36100200-36111000	Weak transcription	Adipose Nuclei	Adipose
23	chr6:36100200-36111000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr6:36100200-36115000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:36100400-36101600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:36100400-36102400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr6:36100400-36103000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:36100400-36104200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:36100400-36107600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:36100400-36107600	Weak transcription	Brain Angular Gyrus	brain
31	chr6:36100400-36107800	Weak transcription	Liver	Liver
32	chr6:36100400-36109400	Weak transcription	Osteobl	bone
33	chr6:36100400-36117400	Weak transcription	Fetal Lung	lung
34	chr6:36100400-36118600	Weak transcription	Small Intestine	intestine
35	chr6:36100600-36101800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
36	chr6:36100600-36101800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr6:36100600-36102000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr6:36100600-36102000	Genic enhancers	HepG2	liver
39	chr6:36100600-36103400	Weak transcription	Spleen	Spleen
40	chr6:36100600-36103800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:36100600-36103800	Weak transcription	GM12878-XiMat	blood
42	chr6:36100600-36104200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr6:36100600-36106000	Weak transcription	NHLF	lung
44	chr6:36100600-36108000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr6:36100600-36108800	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr6:36100600-36110000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr6:36100800-36102000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:36100800-36102000	Strong transcription	Colonic Mucosa	Colon
49	chr6:36100800-36102000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr6:36100800-36103000	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links